The dragon's struggle
by Jedi Kyle Katarn
Summary: After years of absence from Westeros, the son of Rhaegar and Lyanna returns to his place of birth to seek vengeance against his family's butchers. But as he prepares to lead his nation to war, he must also battle the fear of his family's madness within himself. A reimagining of 'Wrath of the North."
1. Chapter 1

**Hi all. I'm back with a new story. My original fic, Wrath of the North, got such great feedback that it inspired me to try my hand at another game of thrones story.**

**So, here are a couple of things you should know**

**1 Jon (Jaehaerys) is the leader of a nation in Essos. He and Daenerys conquered Slaver's bay and chose to start a new kingdom.**

**2 Jon learned the truth of who he is before he left Westeros.**

**3 There is a significant time difference here than in canon. Jon left Westeros at the age of 19, which in this story was several years before the arrival of Robert Baratheon in Winterfell.**

**One last thing. This first chapter is a prologue. The first half of this story will be about how Jaehaerys and Daenerys built their new kingdom, while the second half will focus on their campaign against the Lannisters in Westeros.**

* * *

The night air was warm as the _Shield of Valyria_ cut across the waves of the sea, heading towards Westeros. An ark ship, more than three times the size of a Westerosi ship, it was as much a battleship as it was a transport. The sides lined with rows of cylinder like weapons designed for firing projectiles at other vessels while the hull was reinforced with melted valyrian steel to insure ramming weapons would be utterly useless against it. Its structure was a blend of western and Yi-Ti design, a perfect representation of the blending of multiple cultures that New Valyria was.

Inside the ship were thousands of occupants. Essosi warriors, Unsullied soldiers and Dothraki cavalry. Most terrifying of all, however, were the three adult dragons that were harbored in a massive structure that acted as a resting platform on the deck of the ship. The military of the nation known as New Valyria, gathered together for one goal: the destruction of their leaders' enemies.

One of the two leaders in question was currently standing on the bow of the ship. The king of the restored Valyrian nation was staring out across the sea. To the casual observer, one would think he was quite calm. But the truth was he was feeling a mixture of emotions right now. Eagerness to see his homeland again, worry for the lives of the ones he loved who were accompanying him on this campaign, apprehension at putting those who would be at risk in danger. But there were two feelings that stood out above all. The first was complete rage; rage at those that slaughtered the ones he grew up with. The second was fear; fear that his family's trademark madness may take hold of him as he fought to stamp out his enemies.

"Sam told me I would find you out here."

Jaehaerys Targaryen turned around to see his wife, Daenerys, approaching him. Smiling lightly, he closed the distance between them to wrap her in his arms as she did the same to him. The royal couple held each other for a while before one finally spoke up.

"You know, I always meant to return to Westeros one day. I just never imagined I would be doing so as a would-be conqeror."

Daenerys kissed her husband upon hearing him. "I know" she replied. "Since we met, you wanted to try to build a new life for us far away from our enemies. The vision you had was one where we could live in peace, build a new world where all could live and thrive. Now, we're about to bring down fire and blood on the ones who wronged us."

"Fire and blood. Our family's motto. One of complete destruction."

Daenerys noticed a slight tone of apprehension in Jaehaerys' voice as he spoke. "My love, are you doubting yourself?"

"I'm doubting my reasons for what we are about to do Daenerys."

"What cause could be more noble than helping your family and friends?"

"This campaign is not about trying to liberate people from tyranny, or to give aid to friends. I could have given aid to Robb when I learned he was at war, but I did not do so. I chose to go to war when my sister brought me word of what befell my family. I might have avoided all of what is about to happen if I..." Jaehaerys was suddenly cut off by his wife.

"Can we please not start this again? Jaehaerys, you chose to help the people of our new nation rather than lead them to war when they truly couldn't handle it. Your brother would understand. Now we must help the remaining Starks before any more tragedy befalls them."

"By causing tragedy to befall countless more? Regardless of who wins this war, many will suffer and die as a result of our invasion."

"You didn't care about this when we conquered the slave masters of Dragon's bay, or when we torched them for trying to rebel against us."

Jaehaerys looked away. "Dany, you know what I fear most. Well, aside from anything happening to you or our children."

Daenerys sighed in slight frustration. "Jaehaerys, you are not my father. I am not my father either. The madness will not consume us, no matter how angry we become or what happens to us."

"You say that now with such confidence. Your father probably felt the same about himself at one time. Yet he didn't stay that way. He succumbed to our family's madness, and all suffered for it. The same blood flows through our veins... the same weakness."

Daenerys turned her husband's head back so they were eye to eye once more. "Listen to me. You are no ruthless tyrant. You completely lack the capacity to become such a thing. And I don't say that just because I love you. Ser Barristan, Jorah, Sam, we all believe in you. They would not let you become like my father, and neither will I."

"I know I'm not a tyrant. But..."

"No" Daenerys cut him off. "There is no 'but.' You are NOT a tyrant. Yes, you chose this war in response to your brother's death. Anyone would react the way you did. Your brother acted the same way when his father was killed. You have nothing to be ashamed of."

Jaehaerys was silent following his wife's statement. No matter how much he heard this, he couldn't shake the fear of turning into his grandfather. Since he left Westeros with his best friend years ago, he had fought for a new vision. One where the game of thrones couldn't bring so much pain to people. He hoped to accomplish this by being the ideal ruler, one that always put the needs of the citizens ahead of his personal feelings or desires. But he felt like he was falling too short of that goal, especially with what he was about to do now. He was putting a desire for revenge against House Lannister ahead of the betterment of his and Daenerys' new nation.

"Darling" Daenerys said. "You are going to do this right. No matter what your initial motivation for this was, you will stay on the right path. WE will stay on the right path. Together."

Jaehaerys finally smiled at Dany's words. She always seemed yto know what to say to pull him out of his brooding.

"Thank you Daenerys."

Sharing one last kiss with her husband, Daenerys walked back towards their quarters. Their children would need to be put to bed soon.

Jaehaerys turned one last gaze towards the horizon. Although his conflicting feelings were still there, they no longer had the same hold on him they use to have. Whether they would regain that power or not, he would have to wait and see.

* * *

**The basic overall idea of this story is for Jaehaerys to struggle with his inner rage/madness while trying to stay true to his morals. I'm picturing him as similar to Liu Bei in dynasty warriors (which is itself based off of the ORIGINAL game of thrones, romance of the three kingdoms).**

**Please be sure to review.**

**Also, be sure to check out my Star Wars story "Legacy of the Jedi." PLEASE review, that motivates me to update faster.**


	2. Chapter 2

Jon was walking down the steps of Winterfell's crypts alone, the two guards that were escortinng him staying above ground. Appraently his father gave them orders to bring him here and than stand guard. Jon was so confused as to why he was being called here. He was supposed to be training with Robb, Theon and the other young men of Winterfell. What could his father want, and why was it necessary for them to meet down here?

"Father" Jon called out once he reached the bottom of the stairs. The crypts were as dark as one would expect, the only light coming from the lit torches on the wall.

"Back here, Jon" his father called out. He followed his father's voice into the crypts until he finally found Ned Stark. He was standing at the base of a statue of one of the Stark family members who had already passed on. His father didn't even turn towards him until he was standing right next to him.

"Jon, you know yesterday was your 19th birthday. You are now officially an adult, even if I still consider you and Robb children."

"I know" Jon replied. He turned his head to the statue that was next to them. He was a little surprised to see the name on the plaque: Lyanna Stark. This was his aunt's resting place. The one who was kidnapped by the Targaryen heir, plunging Westeros into a civil war that ended the reign of the Targaryen dynasty.

"Jon" his father said, drawing his attention back to him. "It is time I told you the truth about who you are... and your mother."

Jon thought he was hearing things for a moment. His mother? The one he had asked about his entire life? Jon was so excited that he completely forgot the awkward setting they were in.

"Jon, I love you so much. I want you to know that, no matter what you hear here. You are as much my son as any of my trueborn children." Jon was now confused. Of course he knew his father loved him. True, his father didn't spend as much time with him as he did Robb, but he assumed that was because he was his bastard son and that he didn't want to offend his wife any more than he already had.

"As I'm sure you know, approximately twenty years ago I rode off to war. I had heard that my sister had been kidnapped, and my father and older brother had been murdered by the king for protesting her abduction. I spent a year away from the Vale, where I had been fostered, and by the time I was back in the North I had you with me..."

His father stopped, seeming to be at a loss for words. Jon was still confused; of course he knew all of this. He was about to ask what was going on, until his father spoke up once more.

"I'm sorry, Jon. This is an unpleasant series of memories and I also know what I have to say will bring you much pain. I'm trying to figure out how to tell you this."

Pain? All his life the one thing he wanted more than anything was to know who his mother was.

"Jon, the truth is... your mother was here all along. Not alive, but she was here in Winterfell all these years. In fact, she is right beside us right now."

Jon instinctively looked around for a woman, but saw no one else with them. He was about to ask exactly where she was before he remembered what his father had said. _Not alive_. Slowly, he turned his gaze to the statue next to them. His mother... "Aunt Lyanna..."

"Is not your aunt" his father finished. "She is your mother."

"Are... are you saying you slept with your own sister?"

"No Jon. I am not your real father. I have raised you as such, and I love you as such, but the truth is you are my nephew."

Jon was so shocked he stumbled back and fell on his rear. His father... uncle was by his side in an instant, reaching down and pulling him back up. He felt tears welling up in his eyes. "You mean... you lied to me all these years?"

Tears were now in Ned Stark's eyes as well. "Yes Jon. I'm sorry, but at the time it seemed like the only way to keep you safe."

"Why would I need to be kept safe?"

"Jon, you are a smart young man. Think about this: you are my sister's son. Who do you think that means your real father is?"

Jon realized the truth in an instant. "Rhaegar Targaryen... I am the product of rape."

"No" Lord Stark responded. "Jon, the entire rebellion was a lie. Your father did not kidnap your mother."

Jon nearly fell over again in shock, had Lord Stark not caught him. Sitting both of them on the floor, Lord Stark proceeded to tell his nephew everything he knew. His mother and father had met at the Tourney of Harrenhal, where apparently she had been the famous knight of the laughing tree. Rhaegar had been assigned to find them by his unstable father, and returned saying he never could. In truth, he had found Lyanna. Rhaegar was so impressed with her that he lied to his father to keep her safe from any reprisals for her actions.

At the same time this was going on, Rhaegar's wife Elia Martell of Dorne was pregnant with their second child and her health was failing. Apparently if she survived childbirth this time, she would never survive another childbearing again. Rhaegar felt it was necessary he have a third child, but was unwilling to risk Elia dying. As such, Elia told her husband to find a second wife. She knew how much this meant to her husband, and as long as she and her kids weren't put aside she could tolerate a co-wife. These led to Rhaegar crowning Lyanna Stark the Queen of Love and Beauty after he won the tournament joust.

Lyanna, meanwhile, was bethrothed to Robert Baratheon. However, according to Ned Stark she never wanted this. His mother had heard about Robert's womanizing and knew she could never trust him to remain faithful to her. As such, she was appalled at the idea of marrying him. However, than Rhaegar and Elia came into her life. Rhaegar and Elia had secretly explained their situation to Lyanna and the three ultimately came to an agreement that they all won in: Rhaegar would arrange an agreement with the High Septon to take a second wife and Lyanna would be able to escape her unwanted bethrothal to Rhaegar's whoremongering cousin.

What they hadn't counted on is how their plan would throw Westeros into chaos. Jon knew this story all too well, so his father... uncle, didn't need to explain the rebellion again. What hadn't been known was what happened at the Tower of Joy. Ned explained he had arrived in his sister's chambers to find Lyanna lying in a bed stained with birthing blood, and a several day old baby boy in her arms.

"Me" Jon said.

"Yes, Jon. You. Lyanna confessed everything to me as she was dying."

"You mean... my mother died giving birth to me?" Jon once more felt tears begin to flare up in his eyes.

"Jon, I know what you are thinking right now, and its not your fault. Your mother wasn't just dealing with the complications of childbirth. She also suffered great trauma from what happened to her family. Her father and brother, Rhaegar and Elia, her stepchildren and all the people who ultimately died for nothing on both sides of the rebellion. She was appalled and devestated that she played a part in the events that led to all that suffering. If you combine those with the heartbreak of losing your father and her co-wife's children, she just couldn't handle it all. She wanted to live for you, but she just..."

Ned stopped mid-sentence as he reached up to wipe his eyes, which also had tears flowing out of them. Jon was right there with him. Never... never in his entire life could he imagine this would be the case. Suddenly he thought of something.

"Fa... uncle... are you saying I'm the rightful king of Westeros?"

"Yes. I know I ultimately denied that to you, but your family had too many enemies. Also the realm had just come out of a massive conflict and needed to heal. If I presented you to the realm as the rightful king, you never would have survived to the current day. Robert... I fear that despite his being my friend that he would want you dead, and Tywin Lannister certainly would want you dead. His falling out with the king as well as his daughter's marriage to Robert means he would stop at nothing to be rid of you, just like your siblings."

Jon remembered the story of Rhaenys and Aegon quite well. That story always made him angry, though he never understood why. Well, now he knew.

"Wait. Fa... uncle..."

"Jon, I know what we truly are to each other, but for your own safety you must continue to call me father."

"...Ok. Father, is 'Jon' my real name?"

Ned Stark was silent for a moment before he answered. "No. Your mother named you Jaehaerys. Jaehaerys Targaryen."

Jon was glad he was sitting down. He felt so overwhelmed. "I... father, I need to sit down and think about this for a while."

"I understand. You can stay as long as you want. If you wish to continue speaking about this topic, let me know and I'll arrange for us to do so privately."

His father/uncle got up and took one last look at Lyanna's statue before walking past Jon. However, he stopped after a few steps.

"Jon, I must also say this to you. What we talked about here today, you can not repeat to anyone here in Winterfell, not even Robb or Arya."

* * *

It was midday before Jon walked out of the crypts. He knew he missed his training with Ser Rodrick and the other noble born boys in Winterfell, but he didn't really care about that right now. He was in a slight daze as he walked back to his room from all his fa... uncle told him. He didn't even acknowledge anyone he passed. He only snapped out of it when he got to his room, and someone grabbed him by the shoulder before he could open the door.

"JON!"

Jon turned around and saw Robb was the one holding his shoulder, Theon Greyjoy standing right behind him.

"Oh, sorry brother."

"Are you ok? Theon and I called out to you three times."

"I'm fine. I just... have a lot on my mind right now."

"You missed training this morning Snow" Theon said.

"I was speaking to father."

"Father? What did he want?"

Jon hesitated. Lord Stark had told him he couldn't tell anyone what he had learned today. But, at the same time, this was Robb. Also, he could tell his brother part of what he now knew.

"Father, he... he told me about my mother."

Robb was shocked, and so was Theon.

"What did he say?"

"My mother is dead. Apparently she died giving birth to me." Just saying those words was enough to make tears swell up in his eyes. Jon looked away, not wanting his brother or Theon to see him cry.

No one said anything for a moment. Than, surprisingly, it was Theon who spoke up.

"Sn... Jon, I'm sorry. I know how much the idea of meeting your mother meant to you."

Robb didn't say anything at first. Instead he just stepped forward and pulled Jon into a tight hug. Jon couldn't stop the tears now.

"Jon, I'm so sorry. If you need to talk about this, just let me know."

"Thanks Robb."

"You could talk to me too."

Jon stared at Theon. "Uh... no offense, but..." Theon cut him off.

"Sn... Jon, I know I haven't really been the nicest person towards you, but this is a matter where I can put things aside. I'll be glad to help you in this if there is anything I can do."

Jon was too stunned to really respond. Instead, he gave Theon a grateful nod.

"Jon" Robb said. "I know you probably don't need to be reminded of this, but we are brothers no matter what."

"I know Robb. I also hope you know that if you ever need help, you can count on me."

* * *

Several days past, and Jon's attitude returned to normal. However, at the same time, something about Winterfell felt a bit off. Now that Jon knew the truth about who he was, he felt like he should be doing something more with himself. He had planned on joining the Night's Watch, but now that no longer appealed to him. Yes, the people of the North saw the Night's Watch as a noble order and it was an honor to be in it. But Jon felt like there was something else he could do. Or perhaps a better way to say it was something he should do. While he may have no desire to sit on the Iron Throne, he was a rightful king. Surely there was something more out there for him than to be just another nameless member of an ancient order.

Such thoughts brought him to where he currently was: standing outside Lord Stark's solar waiting to be let in. The door opened, and Lord Stark let him in.

"Jon, is there something I can do for you?"

"Father, I need to talk to you. I... I'm not sure what I should be doing any longer."

Ned was silent for a moment. "What... what do you mean son?"

"Ever since you told me the truth of my parentage, I've been thinking about what I should be doing. I originally wanted to join the Night's Watch, but in light of... what you told me, I think I should consider other options."

"To be honest Jon, I never wanted you in the Night's Watch. Your mother would be waiting for me with a rusty knife if I allowed you to join them. It's just not the place for you."

"Well, the problem I'm having is I can't figure out what it is I should be doing. There must be something more for me out there, but I don't know what."

Ned was silent for a moment. He wasn't sure either. Jon's original birthright was almost certainly out of the question. That would require plunging Westeros into war once again. Ned couldn't let that happen, not while it was nearly two decades since the last war. Westeros needed time to heal.

Than, an idea came to Ned's mind. "Jon, maybe there is someone who can help more than I can. I never told you this, but the Night's Watch does have a member of your family in it, aside from your uncle Benjen."

"Who?"

"His name is Aemon Targaryen. He is a distant uncle of your father, and the current maester of Castle Black. He would be close to a hundred right now, I think. Maybe you should speak with him."

"Castle Black? I thought you said you wanted me to stay away from the Night's Watch."

"I don't want you to join it, but there is nothing wrong with visiting a relative. I can arrange for you to visit Castle Black under the guise of investigating any problems the Night's Watch may have for me. That way you could speak with Aemon without anyone suspecting something."

Jon was liking this idea more and more by the second. "Alright, I think talking to this long lost uncle of mine might help."

**Next time, Jon meets his long lost relative. He also runs into someone else who will play a large role in his future.**

**Reviews help me to update faster, so let me know what you think.**

**Also, please be sure to review my Star Wars story, Legacy of the Jedi. I love seeing people favorite and follow my stories, but the reviews are what I really like to see.**


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